The formation and maintenance mechanism of cognitive biodiversity, that is, community construction, is a core issue in ecological research. Phylogenetic community ecology integrates phylogenetic analysis methods into the analysis of community ecology, providing a new perspective for exploring the evolution and maintenance mechanisms of community biodiversity. Establishing an accurate and reliable community phylogenetic tree is the premise and basis for community phylogenetic analysis. A community phylogenetic tree with lower resolution may lead to biases in the estimation of the phylogenetic diversity index, which in turn affects the inference of specific community ecological processes. At present, the construction of community phylogenetic tree is mainly to use Phylomatic, V.PhyloMaker and other software to generate directory synthetic tree, or to construct molecular phylogenetic tree based on the first generation of DNA barcode fragments. The synthetic tree method does not require steps such as sampling and sequencing, and the cost is low, but there are often more polymorphic branches in the results; the species resolution of the first-generation DNA barcode tree is relatively higher, but the ability to distinguish a large number of the same species is still high. limited. As a second-generation DNA barcode, the chloroplast genome can effectively improve species resolution, and has achieved good results in the reconstruction of phylogenetic relationships of some specific groups. However, the effect of using it in community-level studies has not been tested.
The Molecular Ecology Team of the South China Botanical Garden of the Chinese Academy of Sciences and its collaborators, based on the China Forest Monitoring Network (CForBio) platform, used V.PhyloMaker to monitor 580 species of woody plants in 6 large-scale dynamic monitoring plots in the subtropical evergreen broad-leaved forest area, respectively. A community phylogenetic tree was constructed using software, a first-generation DNA barcode fragment (matK + rbcL + trnH-psbA), and 79 protein-coding genes in the chloroplast genome, and the effects of different tree-building methods on the calculation results of phylogenetic diversity index and functional trait phylogenetic signals were compared. . Studies have shown that using the chloroplast genome as the second-generation DNA barcode to construct a community phylogenetic tree has a significantly better tree-building effect than the first-generation DNA barcode fragment; using the chloroplast genome tree as a reference, compared with the directory tree, the phylogenetic diversity obtained based on the first-generation DNA barcode tree Calculations of phylogenetic signals for exponential and functional traits are more accurate. The study suggests that in communities with a higher proportion of the same species, a higher-resolution chloroplast genome tree should be used as much as possible to obtain more accurate index calculations and ecological inference results.
The relevant research results have been recently published in Molecular Ecology Resources. The research work was funded by the Strategic Pilot Science and Technology Project of the Chinese Academy of Sciences (Type B) and the National Natural Science Foundation of China. The staff of various monitoring platforms provided support and assistance in the process of specimen collection and species identification.